CONFLIST PAA        PAABK PAA01 PAA02 PAA-1

NATOM    PAABK      0
NATOM    PAA01      10
NATOM    PAA02      10
NATOM    PAA-1      9

IATOM    PAA01  CAA 0
IATOM    PAA01  CBA 1
IATOM    PAA01  CGA 2
IATOM    PAA01  O1A 3
IATOM    PAA01  O2A 4
IATOM    PAA01 1HAA 5
IATOM    PAA01 2HAA 6
IATOM    PAA01 1HBA 7
IATOM    PAA01 2HBA 8
IATOM    PAA01  H1A 9
IATOM    PAA02  CAA 0
IATOM    PAA02  CBA 1
IATOM    PAA02  CGA 2
IATOM    PAA02  O1A 3
IATOM    PAA02  O2A 4
IATOM    PAA02 1HAA 5
IATOM    PAA02 2HAA 6
IATOM    PAA02 1HBA 7
IATOM    PAA02 2HBA 8
IATOM    PAA02  H2A 9
IATOM    PAA-1  CAA 0
IATOM    PAA-1  CBA 1
IATOM    PAA-1  CGA 2
IATOM    PAA-1  O1A 3
IATOM    PAA-1  O2A 4
IATOM    PAA-1 1HAA 5
IATOM    PAA-1 2HAA 6
IATOM    PAA-1 1HBA 7
IATOM    PAA-1 2HBA 8

ATOMNAME PAA01    0  CAA
ATOMNAME PAA01    1  CBA
ATOMNAME PAA01    2  CGA
ATOMNAME PAA01    3  O1A
ATOMNAME PAA01    4  O2A
ATOMNAME PAA01    5 1HAA
ATOMNAME PAA01    6 2HAA
ATOMNAME PAA01    7 1HBA
ATOMNAME PAA01    8 2HBA
ATOMNAME PAA01    9  H1A
ATOMNAME PAA02    0  CAA
ATOMNAME PAA02    1  CBA
ATOMNAME PAA02    2  CGA
ATOMNAME PAA02    3  O1A
ATOMNAME PAA02    4  O2A
ATOMNAME PAA02    5 1HAA
ATOMNAME PAA02    6 2HAA
ATOMNAME PAA02    7 1HBA
ATOMNAME PAA02    8 2HBA
ATOMNAME PAA02    9  H2A
ATOMNAME PAA-1    0  CAA
ATOMNAME PAA-1    1  CBA
ATOMNAME PAA-1    2  CGA
ATOMNAME PAA-1    3  O1A
ATOMNAME PAA-1    4  O2A
ATOMNAME PAA-1    5 1HAA
ATOMNAME PAA-1    6 2HAA
ATOMNAME PAA-1    7 1HBA
ATOMNAME PAA-1    8 2HBA






# Made by Junjun Mao 7/11/03
#1.Basic Conformer Information: name, pka, em, rxn.
#23456789A123456789B123456789C
PROTON   PAA01      0
PKA      PAA01      0.0
ELECTRON PAA01      0
EM       PAA01      0.0
RXN      PAA01      -1.60

PROTON   PAA02      0
PKA      PAA02      0.0
ELECTRON PAA02      0
EM       PAA02      0.0
RXN      PAA02      -1.60

PROTON   PAA-1      -1
PKA      PAA-1      4.9
ELECTRON PAA-1      0
EM       PAA-1      0.0
RXN      PAA-1      -18.2

#2.Structure Connectivity
#23456789A123456789B123456789C123456789D123456789E123456789F123456789G123456789H123456789I
#23456789A123456789B123456789C123456789D123456789E123456789F123456789G123456789H123456789I
#ONNECT   conf atom  orbital  ires conn ires conn ires conn ires conn
#ONNECT |-----|----|---------|----|----|----|----|----|----|----|----|----|----|----|----|
CONNECT  PAA01  CAA sp3       -1    C2A 0     CBA 0    1HAA 0    2HAA
CONNECT  PAA01  CBA sp3       0     CAA 0     CGA 0    1HBA 0    2HBA
CONNECT  PAA01  CGA sp2       0     CBA 0     O1A 0     O2A
CONNECT  PAA01  O1A sp3       0     CGA 0     H1A
CONNECT  PAA01  O2A sp2       0     CGA
CONNECT  PAA01 1HAA s         0     CAA
CONNECT  PAA01 2HAA s         0     CAA
CONNECT  PAA01 1HBA s         0     CBA
CONNECT  PAA01 2HBA s         0     CBA
CONNECT  PAA01  H1A s         0     O1A

CONNECT  PAA02  CAA sp3       -1    C2A 0     CBA 0    1HAA 0    2HAA
CONNECT  PAA02  CBA sp3       0     CAA 0     CGA 0    1HBA 0    2HBA
CONNECT  PAA02  CGA sp2       0     CBA 0     O1A 0     O2A
CONNECT  PAA02  O1A sp2       0     CGA
CONNECT  PAA02  O2A sp3       0     CGA 0     H2A
CONNECT  PAA02 1HAA s         0     CAA
CONNECT  PAA02 2HAA s         0     CAA
CONNECT  PAA02 1HBA s         0     CBA
CONNECT  PAA02 2HBA s         0     CBA
CONNECT  PAA02  H2A s         0     O2A

CONNECT  PAA-1  CAA sp3       -1    C2A 0     CBA 0    1HAA 0    2HAA
CONNECT  PAA-1  CBA sp3       0     CAA 0     CGA 0    1HBA 0    2HBA
CONNECT  PAA-1  CGA sp2       0     CBA 0     O1A 0     O2A
CONNECT  PAA-1  O1A sp2       0     CGA
CONNECT  PAA-1  O2A sp2       0     CGA
CONNECT  PAA-1 1HAA s         0     CAA
CONNECT  PAA-1 2HAA s         0     CAA
CONNECT  PAA-1 1HBA s         0     CBA
CONNECT  PAA-1 2HBA s         0     CBA

#3.Atom Parameters: Partial Charges and Radii
# Radii from "Bondi, J.Phys.Chem., 68, 441, 1964."
RADIUS   PAA    CAA 1.70
RADIUS   PAA    CBA 1.70
RADIUS   PAA    CGA 1.70
RADIUS   PAA    O1A 1.52
RADIUS   PAA    O2A 1.52
RADIUS   PAA   1HAA 1.20
RADIUS   PAA   2HAA 1.20
RADIUS   PAA   1HBA 1.20
RADIUS   PAA   2HBA 1.20
RADIUS   PAA    H1A 1.20
RADIUS   PAA    H2A 1.20

CHARGE   PAA01  CBA  0.000
CHARGE   PAA01  CGA  0.550
CHARGE   PAA01  O1A -0.475
CHARGE   PAA01  O2A -0.475
CHARGE   PAA01  H1A  0.400

CHARGE   PAA02  CBA  0.000
CHARGE   PAA02  CGA  0.550
CHARGE   PAA02  O1A -0.475
CHARGE   PAA02  O2A -0.475
CHARGE   PAA02  H2A  0.400

CHARGE   PAA-1  CBA -0.160
CHARGE   PAA-1  CGA  0.360
CHARGE   PAA-1  O1A -0.600
CHARGE   PAA-1  O2A -0.600

#=========================================================================
#        GRP   #      BOND     AFFECTED_ATOMS
#123456789012345678901234567890
#-------|---|----|-|---------|----|----|----|----|----|----|----|----|----
ROTAMER  PAA   0     C2A- CAA  CBA  CGA  O1A  O2A
ROTAMER  PAA   1     CAA- CBA  CGA  O1A  O2A
ROTAMER  PAA   2     CBA- CGA  O1A  O2A
#=========================================================================

